SMTL ID : 5eru.1

Ternary complex of GephE - ADP - Molybdenum cluster

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

10 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 5 residues within 4Å: Chain A: C.152, V.153, L.154, A.155 Chain B: S.385 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.385 ACT.2: 4 residues within 4Å: Chain A: T.25, A.39, K.156, N.179 No protein-ligand interaction detected (PLIP) ACT.3: 6 residues within 4Å: Chain A: M.19, T.20, P.21, V.22, R.301, K.328 3 PLIP interactions: 3 interactions with chain A Water bridges: A:V.22, A:K.328 Salt bridges: A:K.328 ACT.4: 4 residues within 4Å: Chain A: L.6, T.7, S.8, F.283 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.283 ACT.5: 7 residues within 4Å: Chain A: N.310, P.311, V.312 Chain B: L.48, R.141, D.146 Ligands: MPD.8 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Water bridges: B:R.141, A:N.310 Salt bridges: B:R.141 ACT.22: 5 residues within 4Å: Chain A: S.385 Chain B: C.152, V.153, L.154, A.155 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.385 ACT.23: 4 residues within 4Å: Chain B: T.25, A.39, K.156, N.179 No protein-ligand interaction detected (PLIP) ACT.24: 6 residues within 4Å: Chain B: M.19, T.20, P.21, V.22, R.301, K.328 3 PLIP interactions: 3 interactions with chain B Water bridges: B:V.22, B:K.328 Salt bridges: B:K.328 ACT.25: 4 residues within 4Å: Chain B: L.6, T.7, S.8, F.283 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.283 ACT.26: 7 residues within 4Å: Chain A: L.48, R.141, D.146 Chain B: N.310, P.311, V.312 Ligands: MPD.29 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Water bridges: B:N.310, A:R.141 Salt bridges: A:R.141

6 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.6: 10 residues within 4Å: Chain A: M.9, D.10, F.13, L.320, R.336, P.337, I.339, Y.356, M.394, M.414 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.13, A:P.337, A:I.339 Hydrogen bonds: A:D.10 Water bridges: A:Y.356, A:Y.356 MPD.7: 4 residues within 4Å: Chain A: N.195, E.197, R.210 Chain B: R.31 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.195, B:R.31 Water bridges: A:N.195, A:R.210 MPD.8: 13 residues within 4Å: Chain A: S.208, T.212, P.311, V.312, V.315, R.358 Chain B: L.48, I.147, S.163, G.166, L.167, T.170 Ligands: ACT.5 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:T.212, A:P.311, B:L.167 Hydrogen bonds: A:R.358, A:R.358 MPD.27: 10 residues within 4Å: Chain B: M.9, D.10, F.13, L.320, R.336, P.337, I.339, Y.356, M.394, M.414 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.13, B:P.337, B:I.339 Water bridges: B:Y.356, B:Y.356 MPD.28: 4 residues within 4Å: Chain A: R.31 Chain B: N.195, E.197, R.210 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.195, A:R.31 Water bridges: B:N.195, B:R.210 MPD.29: 13 residues within 4Å: Chain A: L.48, I.147, S.163, G.166, L.167, T.170 Chain B: S.208, T.212, P.311, V.312, V.315, R.358 Ligands: ACT.26 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:T.212, B:P.311, A:L.167 Hydrogen bonds: B:R.358, B:R.358

2 x CA: CALCIUM ION(Non-functional Binders)

CA.9: 2 residues within 4Å: Chain A: G.256 Ligands: ADP.10 No protein-ligand interaction detected (PLIP) CA.30: 2 residues within 4Å: Chain B: G.256 Ligands: ADP.31 No protein-ligand interaction detected (PLIP)

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.10: 26 residues within 4Å: Chain A: S.188, T.189, E.192, L.193, I.205, R.206, D.207, S.208, N.209, R.210, S.254, G.255, G.256, V.257, S.258, D.263, P.289, P.308, G.309, N.310, P.311 Chain B: T.96, G.97, R.141 Ligands: CA.9, MG.21 25 PLIP interactions: 5 interactions with chain B, 20 interactions with chain A Hydrogen bonds: B:R.141, A:S.188, A:E.192, A:D.207, A:S.208, A:S.208, A:N.209, A:G.255, A:G.256, A:V.257, A:S.258, A:S.258, A:G.309 Water bridges: B:T.96, B:T.96, B:G.97, B:G.97, A:E.192, A:E.192, A:N.209, A:N.209, A:S.258, A:S.258, A:S.258, A:N.310 ADP.31: 26 residues within 4Å: Chain A: T.96, G.97, R.141 Chain B: S.188, T.189, E.192, L.193, I.205, R.206, D.207, S.208, N.209, R.210, S.254, G.255, G.256, V.257, S.258, D.263, P.289, P.308, G.309, N.310, P.311 Ligands: CA.30, MG.42 26 PLIP interactions: 5 interactions with chain A, 21 interactions with chain B Hydrogen bonds: A:R.141, B:S.188, B:D.207, B:D.207, B:S.208, B:S.208, B:N.209, B:G.255, B:G.256, B:V.257, B:S.258, B:S.258, B:G.309 Water bridges: A:T.96, A:T.96, A:G.97, A:G.97, B:E.192, B:E.192, B:N.209, B:N.209, B:S.258, B:S.258, B:S.258, B:D.263, B:N.310

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.11: 6 residues within 4Å: Chain A: V.183, S.246, R.247, A.248, D.249, K.302 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.247, A:D.249, A:D.249 Water bridges: A:K.302, A:K.302 Salt bridges: A:K.302 PO4.32: 6 residues within 4Å: Chain B: V.183, S.246, R.247, A.248, D.249, K.302 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.247, B:D.249, B:D.249 Water bridges: B:K.302, B:K.302 Salt bridges: B:K.302

16 x MO: MOLYBDENUM ATOM(Non-covalent)(Non-functional Binders)

MO.12: 10 residues within 4Å: Chain A: P.286, G.287, L.288, R.353 Ligands: MO.13, MO.14, MO.16, MO.17, MO.19, MOO.20 Ligand excluded by PLIP MO.13: 5 residues within 4Å: Chain A: L.288, R.353 Ligands: MO.12, MO.14, MO.16 Ligand excluded by PLIP MO.14: 5 residues within 4Å: Chain A: P.289 Ligands: MO.12, MO.13, MO.19, MOO.20 Ligand excluded by PLIP MO.15: 6 residues within 4Å: Chain A: N.310, S.313 Ligands: MO.17, MO.18, MO.19, MOO.20 Ligand excluded by PLIP MO.16: 5 residues within 4Å: Chain A: R.353 Ligands: MO.12, MO.13, MO.17, MO.19 Ligand excluded by PLIP MO.17: 7 residues within 4Å: Chain A: K.285, P.286 Ligands: MO.12, MO.15, MO.16, MO.19, MOO.20 Ligand excluded by PLIP MO.18: 3 residues within 4Å: Chain B: V.55 Ligands: MO.15, MO.19 Ligand excluded by PLIP MO.19: 7 residues within 4Å: Ligands: MO.12, MO.14, MO.15, MO.16, MO.17, MO.18, MOO.20 Ligand excluded by PLIP MO.33: 10 residues within 4Å: Chain B: P.286, G.287, L.288, R.353 Ligands: MO.34, MO.35, MO.37, MO.38, MO.40, MOO.41 Ligand excluded by PLIP MO.34: 5 residues within 4Å: Chain B: L.288, R.353 Ligands: MO.33, MO.35, MO.37 Ligand excluded by PLIP MO.35: 5 residues within 4Å: Chain B: P.289 Ligands: MO.33, MO.34, MO.40, MOO.41 Ligand excluded by PLIP MO.36: 6 residues within 4Å: Chain B: N.310, S.313 Ligands: MO.38, MO.39, MO.40, MOO.41 Ligand excluded by PLIP MO.37: 5 residues within 4Å: Chain B: R.353 Ligands: MO.33, MO.34, MO.38, MO.40 Ligand excluded by PLIP MO.38: 7 residues within 4Å: Chain B: K.285, P.286 Ligands: MO.33, MO.36, MO.37, MO.40, MOO.41 Ligand excluded by PLIP MO.39: 3 residues within 4Å: Chain A: V.55 Ligands: MO.36, MO.40 Ligand excluded by PLIP MO.40: 7 residues within 4Å: Ligands: MO.33, MO.35, MO.36, MO.37, MO.38, MO.39, MOO.41 Ligand excluded by PLIP

2 x MOO: MOLYBDATE ION(Non-covalent)

MOO.20: 12 residues within 4Å: Chain A: P.286, G.287, L.288, P.289, P.308, N.310, S.313 Ligands: MO.12, MO.14, MO.15, MO.17, MO.19 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.287, A:L.288, A:S.313 Water bridges: A:G.309, A:N.310 MOO.41: 12 residues within 4Å: Chain B: P.286, G.287, L.288, P.289, P.308, N.310, S.313 Ligands: MO.33, MO.35, MO.36, MO.38, MO.40 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.287, B:L.288, B:S.313 Water bridges: B:G.309, B:N.310

2 x MG: MAGNESIUM ION(Non-covalent)

MG.21: 5 residues within 4Å: Chain A: G.256, S.258, D.263 Chain B: T.96 Ligands: ADP.10 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.263, H2O.2, H2O.5, H2O.18 MG.42: 5 residues within 4Å: Chain A: T.96 Chain B: G.256, S.258, D.263 Ligands: ADP.31 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.263, H2O.1, H2O.18, H2O.22

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kasaragod, V.B. et al., Structural Framework for Metal Incorporation during Molybdenum Cofactor Biosynthesis. Structure (2016)

Release Date

2016-05-04

Peptides

Gephyrin: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Gephyrin

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